Build the “composite“ life stages ontology directly in Uberon #3021
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Basic ODK workflow | |
| name: CI | |
| # Controls when the action will run. | |
| on: | |
| # Triggers the workflow on push or pull request events but only for the master branch | |
| push: | |
| branches: [ master ] | |
| paths: | |
| - 'src/**' | |
| pull_request: | |
| branches: [ master ] | |
| paths: | |
| - 'src/**' | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| # This workflow contains a single job called "ontology_qc" | |
| ontology_qc: | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| container: obolibrary/odkfull:v1.5.3 | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v3 | |
| - name: Run ontology QC checks | |
| id: check | |
| continue-on-error: true | |
| env: | |
| DEFAULT_BRANCH: master | |
| ROBOT_JAVA_ARGS: -Xmx6G | |
| run: cd src/ontology && mkdir -p tmp reports mirror && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' GH_ACTION=true BRI=true MIR=false IMP=false test > TESTLOG.log | |
| - name: Reason over taxon constraints | |
| id: explaintc | |
| continue-on-error: true | |
| if: steps.check.outcome == 'failure' | |
| run: | | |
| if [ -s src/ontology/reports/taxon-constraint-check.txt ]; then | |
| robot explain -i src/ontology/tmp/uberon-edit-plus-tax-equivs.owl -M unsatisfiability -u all -r ELK -e taxon-unsats.md | |
| echo "<details>\n<summary>This PR violates some taxon constraints. Here is what the reasoner has to say:</summary>\n" > comment.md | |
| cat taxon-unsats.md >> comment.md | |
| echo "</details>" >> comment.md | |
| exit 1 | |
| fi | |
| - name: Post explanation for taxon constraint violations | |
| if: steps.explaintc.outcome == 'failure' | |
| uses: NejcZdovc/comment-pr@v2 | |
| with: | |
| github_token: ${{secrets.GITHUB_TOKEN}} | |
| file: "../../comment.md" | |
| identifier: "TAXON_CONSTRAINTS_REASONING" | |
| - name: Last rows of QC report | |
| if: steps.check.outcome == 'failure' | |
| run: | | |
| tail -20 src/ontology/TESTLOG.log | |
| exit 1 |